Class diagram restructuring with GROOVE

This paper describes the GROOVE solution to the "Class Diagram Restructuring" case study of the Tool Transformation Contest 2013. We show that the visual rule formalism enables the required restructuring to be formulated in a very concise manner. Moreover, the GROOVE functionality for state space exploration allows checking confluence. Performance-wise, however, the solution does not scale well

Flow Diagram Decomposition Using Graph Transformations

The key challenge of model transformations in model-driven development is in transforming higher-level abstract models into more concrete ones that can be used to generate implementation level models, including executable business process representations and program code. Many of the modelling languages (like UML Activity Diagrams or BPMN) use unstructured flow graphs to describe the operation sequence of a business process. If a structured language is chosen as the executable representation, it is difficult to compile the unstructured flows into structured statements. Even if a target language structure contains goto-like statements it is often simpler and more efficient to deal with programs that have structured control flow to make the executable representation more understandable. In this paper, we take a first step towards an implementation of existing decomposition methods using graph transformations, and we evaluate their effectiveness with a view to readability and essential complexity measures

Towards model structuring based on flow diagram decomposition

The key challenge of model transformations in model-driven development is in transforming higher-level abstract models into more concrete ones that can be used to generate implementation level models, including executable business process representations and program code. Many of the modelling languages (like UML Activity Diagrams or BPMN) use unstructured flow graphs to describe the operation sequence of a business process. If a structured language is chosen as the executable representation, it is difficult to compile the unstructured flows into structured statements. Even if a target language structure contains goto-like statements it is often simpler and more efficient to deal with programs that have structured control flow to make the executable representation more understandable. In this paper, we take a first step towards an implementation of existing decomposition methods using graph transformations, and we evaluate their effectiveness with a view to readability and essential complexity measures

Refactoring of UML models using AGG

Model refactoring is an emerging research topic that is heavily inspired by refactoring of object-oriented programs. Current-day UML modeling environments provide poor support for evolving UML models and applying refactoring techniques at model level. As UML models are intrinsically graph-based in nature we propose to use graph transformations to specify and apply model refactoring. More in particular, we use a specific graph transformation tool, AGG, and provide recommendations of how AGG may be improved to better support model refactoring. These recommendations are based on a small experiment that we have carried out with refactoring of UML class diagrams and state machines

Grey Areas: Songs of Memory, Imagination, Intellect, and Death for Baritone Voice and Mixed Instrumental Octet

The central element of this thesis is Grey Areas, a newly-composed dramatic piece in four movements for baritone and chamber ensemble. The work is highly personal in both its subject matter and its musical execution; it also contains a unique movement order that changes depending on the age of the baritone. Along with the written portion of this document and full score, I completed a studio recording of the entire composition as part of the project. Composers (by necessity) are more frequently functioning as their own recording and mixing engineers for their own works. I have been able to gather a variety of skills related to the recording arts and sought out opportunities to employ them in this project. In order to meaningfully add to the greater body of research, I describe both the creative aspects of my compositional process and the technical aspects of the recording process

Developing molecular tools for probing and modulating genomic spatial adjacency

In addition to the vast information encoded in DNA sequence, the genome has physical features that are also essential for its function, including its organization in threedimensional space. The development of high-throughput technology has greatly advanced our understanding of the spatial organization of the genome but has also raised more questions. In this thesis, we developed molecular tools to address the remaining challenges regarding the interplay between genomic organization and function. By breaking down the subject from the global architecture of the genome into an ensemble of spatially adjacent chromatin segments, we came up with different methods covering various aspects. We demonstrated in Paper I that global spatial information can be transferred in the format of DNA sequence encoding pairwise spatial proximity between two distinct molecular objects. We have shown that by growing network from pairwise relationship encoded in DNA sequence, spatial features at a global scale can be recovered. The results from this work highlighted the potential of using pairwise adjacency as a fundamental unit for recording the spatial organization of complex molecular systems. The high programmability and versatility of nucleic acids make them an ideal medium for encoding this information. With the aim of studying the pairwise relationship between genomic DNA in cells, we devised a CRISPR-dCas9 system for different purposes by leveraging its high programmability for genome targeting. In Paper III, we have shown that the re-designed guide RNA can direct dCas9 to a pair of genomic loci, inducing DNA contacts. This system can be applied as a modulation tool to introduce pairwise contacts for decoding functional implications in cells. In Paper IV, we developed a method for the direct detection of pairwise interactions between genomic loci at the single-cell level in situ. This method is achieved by conjugating oligonucleotide tags to Cas9 and using the tags for probing the spatial adjacency between a pair of genomic loci targeted by Cas9 Meanwhile, we developed an efficient method to fabricate and purify DNA origami with modifications in Paper II. This method makes the production of functionalized nanostructures more time and material-efficient compared to established techniques. The ease of production allows broader applications of functionalized nanostructures, including characterizing the effect of nanoscale distance on biochemical assays, as shown in Paper IV

A UML/OCL framework for the analysis of fraph transformation rules

In this paper we present an approach for the analysis of graph transformation rules based on an intermediate OCL representation. We translate different rule semantics into OCL, together with the properties of interest (like rule applicability, conflicts or independence). The intermediate representation serves three purposes: (i) it allows the seamless integration of graph transformation rules with the MOF and OCL standards, and enables taking the meta-model and its OCL constraints (i.e. well-formedness rules) into account when verifying the correctness of the rules; (ii) it permits the interoperability of graph transformation concepts with a number of standards-based model-driven development tools; and (iii) it makes available a plethora of OCL tools to actually perform the rule analysis. This approach is especially useful to analyse the operational semantics of Domain Specific Visual Languages. We have automated these ideas by providing designers with tools for the graphical specification and analysis of graph transformation rules, including a backannotation mechanism that presents the analysis results in terms of the original language notation